Administering pathway tools
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Administering Pathway Tools. Obtaining Pathway Tools. Free to non-commercial organizations To obtain license agreement go to BioCyc.org and click on Software/Database Download Follow Installation Guide ptools-local directory Locate in common directory

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Obtaining pathway tools
Obtaining Pathway Tools

  • Free to non-commercial organizations

  • To obtain license agreement go to BioCyc.org and click on Software/Database Download

  • Follow Installation Guide

  • ptools-local directory

    • Locate in common directory

    • PGDBs created by all users who use this ptools installation

    • PGDBs downloaded via the registry

    • ptools-init.dat for this ptools installation


New pathway tools releases
New Pathway Tools Releases

  • Major releases = External software releases

    • Twice per year

    • Announced on ptools-users mailing list

  • Minor releases twice per year affect only our BioCyc.org Web site and flatfile distributions

  • We support one prior release only

  • Releases announced on [email protected]

  • Read release notes at

    • http://brg.ai.sri.com/ptools/release-notes.html

  • Install process:

    • Upgrade schema of your DB (software assisted)


Pgdb storage file or relational database
PGDB Storage:File or Relational Database

  • File storage:

    • Advantages:

      • No RDBMS installation and configuration

    • Disadvantages:

      • Must be loaded and saved in its entirety

      • No transaction history

      • No concurrent access for multiple users

  • Oracle/MySQL storage:

    • Advantages:

      • Faster read access, faster saves

      • Concurrent update access for multiple users

      • Stores history of all PGDB updates

    • Disadvantages:

      • RDBMS must be installed and configured


Multiuser access to pgdbs
Multiuser Access to PGDBs

  • PGDB stored within one Oracle or MySQL server

  • Each curator installs PTools on their workstation

  • Different curators can use different software platforms

  • Workstations query RDBMS server via internet

  • Local disk cache speeds access

  • For each frame access, PTools queries

    • In-memory cache, disk cache, RDBMS server

  • After curator saves changes, all changes made by other users are loaded into curator’s session


How to release a pgdb
How to Release a PGDB?

  • Decide on release frequency and schedule

    • Don’t wait until it’s perfect to release it!

  • Freeze curation for 1 week

  • Quality assurrance

    • Run consistency checker

      • Tools -> Consistency Checker

      • Also updates organism-summary statistics

  • Update publications, authors in organism frame

    • Update via Organism editor

  • Create new version of PGDB

    • ptools-local/pgdbs/yeastcyc/1.0/kb/yeastbase.ocelot

    • Edit against the new version, release the old version

  • Author release notes

  • Register PGDB in SRI PGDB registry

    • Will allow SRI to include it in BioCyc


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